NBDC Research ID: hum0094.v3

 

SUMMARY

Aims: Identification of oncogenic alteration in breast cancer, lung adenocarcinoma and colorectal cancer (CRC) through genomic analysis.

Methods: Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-seq were performed with HiSeq 2000/2500. Methylation analysis was performed with Infinium MethylationEPIC Kit. SNP array was performed with HumanOmni2.5-8.

Participants/Materials: Surgically resected breast cancer, lung adenocarcinoma and CRC tissues and paired non-tumor tissues or peripheral blood cells (as normal tissues)

            WES: Triple negative breast cancer: 36 cases (including 16 cases used for WGS and 23 cases used for RNA-seq)

                       Lung adenocarcinoma : 43 cases

                       CRC : 149 cases

            WGS: Triple negative breast cancer: 16 cases 

            RNA-seq: Triple negative breast cancer: 23 cases

                            Estrogen receptor-positive breast cancer: 17 cases

                            Human epidermal growth factor receptor 2 (HER2)-positive breast cancer: 15 cases

                            Lung adenocarcinoma : 43 cases

                            CRC : 94 cases

            RNA access: CRC: 18 cases

            Methylation array: CRC: 93 cases

            SNP array: CRC: 25 cases

URL: http://mano-lab.umin.jp/english/index.html

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000095 NGS (WGS, Exome, RNA-seq) Controlled Access (Type I) 2017/09/04
JGAS00000000105 NGS (Exome, RNA-seq) Controlled Access (Type I) 2018/01/22
JGAS00000000113

NGS (Exome, RNA-seq, RNA access),

Methylation array, SNP array

Controlled Access (Type I) 2019/02/12

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

WGS

Participants/Materials Triple negative breast cancer (ICD10: C50): 16 cases
Targets WGS
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source DNAs extracted from tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues
Cell Lines -
Library Construction (kit name) NEBNext® Ultra™ DNA Library Prep Kit for Illumina®
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 103 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000095
Total Data Volume 8 TB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

Exome

Participants/Materials

Triple negative breast cancer (ICD10: C50): 36 cases

Lung adenocarcinoma (ICD10: C349): 43 cases

CRC (ICD10: C18, 19, 20): 149 cases

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source DNAs extracted from tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues
Cell Lines -
Library Construction (kit name) NEBNext® Ultra™ DNA Library Prep Kit for Illumina®, SureSelect Human All Exon V5
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)

breast cancer and lung adenocarcinoma: 103 bp

CRC: 104 bp or 135 bp

Japanese Genotype-phenotype Archive Data set ID

Triple negative breast cancer: JGAD00000000095

Lung adenocarcinoma: JGAD00000000110 (bam)

CRC: JGAD00000000122 (bam)

Total Data Volume 15 TB (bam [ref: hg19/hg38])
Comments (Policies)

NBDC policy (JGAD00000000095, JGAD00000000122)

NBDC policy & Company User Limit (JGAD00000000110)

 

RNA-seq

Participants/Materials

Triple negative breast cancer (ICD10: C50): 23 cases

Estrogen receptor-positive breast cancer (ICD10: C50): 17 cases

HER2-positive breast cance (ICD10: C50)r: 15 cases

Lung adenocarcinoma (ICD10: C349): 43 cases

CRC (ICD10: C18, 19, 20): 94 cases

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source RNAs extracted from tumor tissues
Cell Lines -
Library Construction (kit name) NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®
Fragmentation Methods Heat treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)

breast cancer and lung adenocarcinoma: 103 bp

CRC: 104 bp or 135 bp

Japanese Genotype-phenotype Archive Data set ID

Breast cancers: JGAD00000000095

Lung adenocarcinoma: JGAD00000000111 (fastq)

CRC: JGAD00000000122 (fastq)

Total Data Volume 15 TB (fastq)
Comments (Policies)

NBDC policy (JGAD00000000095, JGAD00000000122)

NBDC policy & Company User Limit (JGAD00000000111)

 

RNA access

Participants/Materials CRC (ICD10: C18, 19, 20): 18 cases
Targets RNA access
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source RNAs extracted from tumor tissues
Cell Lines -
Library Construction (kit name) TruSeq® RNA Access Library Prep Kit
Fragmentation Methods Heat treatment
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 104 bp or 135 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000122 (fastq)
Total Data Volume 5 TB (fastq)
Comments (Policies) NBDC policy

 

Methylation array

Participants/Materials

CRC (ICD10: C18, 19, 20): 93 cases

normal tissues: 20 samples

Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina [Infinium Human MethylationEPIC BeadChip]
Source DNAs extracted from tumor tissues and paired non-tumor tissues
Cell Lines -
Library Construction (kit name) Infinium Human MethylationEPIC BeadChip Kit
Algorithms for Calculating Methylation-rate (software) GenomeStudio (Illumina)
Filtering Methods Detection P-value >= 0.05
Normalization of microarray -
Probe Number 867,926 Probe Numbers
Japanese Genotype-phenotype Archive Data set ID JGAD00000000122
Total Data Volume 5 TB (tsv)
Comments (Policies) NBDC policy

 

SNP array

Participants/Materials: CRC (ICD10: C18, 19, 20): 25 cases
Targets genome wide CNVs
Target Loci for Capture Methods -
Platform Illumina [HumanOmni2.5-8 BeadChip]
Source DNAs extracted from tumor tissues and paired non-tumor tissues
Cell Lines -
Library Construction (kit name) Infinium HumanOmni2.5-8 kit
Algorithm for detecting CNVs (software) GenomeStudio (Illumina)
Filtering Methods As described in 'Illumine Infinium Assay Ver.2.1.'
CNV number -
Japanese Genotype-phenotype Archive Data set ID JGAD00000000122
Total Data Volume 5 TB (tsv)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Hiroyuki Mano

Affiliation: Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo

Project / Group Name: -

URL: http://mano-lab.umin.jp/english/index.html

Funds / Grants (Research Project Number):

NameTitleProject Number
Leading Advanced Projects for medical innovation, The Japan Agency for Medical Research and Development (AMED) Project for novel therapeutic targets in cancer -
KAKENHI Grant-in-Aid for Scientific Research (C) Oncogenic mutations of RAC small GTPases in Human cancers 26430106
Grant from The Princess Takamatsu Cancer Research Fund Analysis of molecular mechanisms of oncogenic activity of RAC small GTPase -
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Elucidation of initiation and progression mechanism of human epithelial tumors towards identification of novel therapeutic targets JP17cm0106502

 

PUBLICATIONS

TitleDOIData Set ID
1 Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency doi: 10.1371/journal.pgen.1006853 JGAD00000000095
2 Inactivating mutations and hypermethylation of the NKX2-1/TTF-1 gene in non-terminal respiratory unit-type lung adenocarcinomas. doi: 10.1111/cas.13313 JGAD00000000110, JGAD00000000111
3 Fusion Kinases Identified by Genomic Analyses of Sporadic Microsatellite Instability-High Colorectal Cancers doi: 10.1158/1078-0432.CCR-18-1574 JGAD00000000122

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use